# Looper: Duplicate sample name error

I am using Looper. While running looper run project_config.yaml I am getting duplicate sample name error. I have two fastq files for each sample, so in the annotation.csv file I have:

sample_name,library,file
abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r1.fq.gz
abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r2.fq.gz
abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r1.fq.gz
abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r2.fq.gz


My pipeline_interface.yaml file looks the following way:

protocol_mapping:
RNA-seq: sandro_rna_seq

pipelines:
sandro_rna_seq:
name: sandro_rna_seq
path: sandro_rna_seq.py  # relative to this
pipeline_interface.yaml file
looper_args: True
arguments:
"-L": "IU"
"-T": "gencode_mouse_m13"
"-E": "/scratch/nv4e/binf-
"-C": "/scratch/nv4e/binf-
pipelines/bulk_rna_seq/salmon/pypiper/salmon_rna_seq.yaml"
"-X": "True"
"-P": "6"
"-I": sample_name
resources:
default:
file_size: "0"
cores: "20"
mem: "120000"


Why am I getting this error? How could I fix it?

As explained in the pep docs, the sample_name column should be considered a unique identifier for a sample. The PEP requires that One row corresponds to one sample You have multiple rows with the same name; this is not allowed.
You simply need to recast your annotation sheet such that it has file1 and file2 columns, but only 2 rows.